Arabidopsis thaliana vs Olea europaea var. sylvestris LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Olea europaea var. sylvestris (Olea europaea var. sylvestris, O_europaea_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterArabidopsis thalianaOlea europaea var. sylvestris
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 210,672 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 81,212,045 out of 119,667,750
Covered: 38,455,705 out of 119,667,750

Uncovered: 8,980,949 out of 33,775,569
Matches: 15,519,812 out of 33,775,569
Mismatches: 8,724,131 out of 33,775,569
Insertions: 550,677 out of 33,775,569
Identity over aligned base-pairs: 62.6%

Olea europaea var. sylvestris

Uncovered: 1,076,944,662 out of 1,140,989,389
Covered: 64,044,727 out of 1,140,989,389

Uncovered: 22,364,326 out of 52,755,300
Matches: 20,318,634 out of 52,755,300
Mismatches: 9,295,019 out of 52,755,300
Insertions: 777,321 out of 52,755,300
Identity over aligned base-pairs: 66.9%

Block size distribution

Size range All 210,672 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,717
9.1 kb
10 bp - 100 bp
33,024
2.3 Mb
10,168
725.8 kb
100 bp - 1 kb
161,798
53.6 Mb
55,116
21.0 Mb
1 kb - 10 kb
14,049
24.4 Mb
25,444
56.2 Mb
10 kb - 100 kb
84
1.2 Mb
252
3.5 Mb